N scaling is a go... like 90 percent sure

mazeau · Apr 2, 2019 · f6354b0 · rwest · Apr 17, 2019 · mazeau
1 parent 1e71dba
commit f6354b0
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Showing 2 changed files with 16 additions and 12 deletions.
diff --git a/rmgpy/data/thermo.py b/rmgpy/data/thermo.py
@@ -1272,19 +1272,19 @@ def setDeltaAtomicAdsorptionEnergies(self, bindingEnergies):
         # this depends on the two metal surfaces, the reference one
         # used in the database of adsorption energies, and the desired surface
         # These are the reference ones, Ni(111), from Blaylock's supplementary material
-        deltaAtomicAdosrptionEnergy = {
-            'C': rmgpy.quantity.Energy(-5.997, 'eV/molecule'),
-            'H': rmgpy.quantity.Energy(-2.778, 'eV/molecule'),
-            'O': rmgpy.quantity.Energy(-4.485, 'eV/molecule')
-        }
+        # deltaAtomicAdosrptionEnergy = {
+        #     'C': rmgpy.quantity.Energy(-5.997, 'eV/molecule'),
+        #     'H': rmgpy.quantity.Energy(-2.778, 'eV/molecule'),
+        #     'O': rmgpy.quantity.Energy(-4.485, 'eV/molecule')
+        # }
         # These are for Pt, from Katrin
         deltaAtomicAdosrptionEnergy = {
             'C': rmgpy.quantity.Energy(-6.750, 'eV/molecule'),
             'H': rmgpy.quantity.Energy(-2.479, 'eV/molecule'),
             'O': rmgpy.quantity.Energy(-3.586, 'eV/molecule'),
             'N': rmgpy.quantity.Energy(-4.352, 'eV/molecule'),
         }
-        for element in 'CHO':
+        for element in 'CHON':
             deltaAtomicAdosrptionEnergy[element].value_si =  bindingEnergies[element].value_si - deltaAtomicAdosrptionEnergy[element].value_si
         self.deltaAtomicAdsorptionEnergy = deltaAtomicAdosrptionEnergy
 
@@ -1332,7 +1332,7 @@ def correctBindingEnergy(self, thermo, species):
             findCp0andCpInf(species, thermo)
 
         ## now edit the adsorptionThermo using LSR
-        for element in 'CHO':
+        for element in 'CHON':
             changeInBindingEnergy = self.deltaAtomicAdsorptionEnergy[element].value_si * normalizedBonds[element]
             thermo.H298.value_si += changeInBindingEnergy
         thermo.comment += " Binding energy corrected by LSR."
@@ -1381,6 +1381,9 @@ def getThermoDataForSurfaceSpecies(self, species):
                 elif bond.isTriple():
                     bondedAtom.incrementRadical()
                     bondedAtom.incrementLonePairs()
+                elif bond.isQuadruple():
+                    bondedAtom.incrementRadical()
+                    bondedAtom.incrementLonePairs()
                 else:
                     raise NotImplementedError("Can't remove surface bond of type {}".format(bond.order))
 

diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
@@ -117,14 +117,15 @@ def convertBindingEnergies(bindingEnergies):
     :return: the processed and checked dictionary
     """
     if bindingEnergies is None:
-        bindingEnergies = { # default values for Ni(111)
-                       'C':(-5.997, 'eV/molecule'),
-                       'H':(-2.778, 'eV/molecule'),
-                       'O':(-4.485, 'eV/molecule'),
+        bindingEnergies = { # default values for Pt(111)
+                       'C':(-6.750, 'eV/molecule'),
+                       'H':(-2.479, 'eV/molecule'),
+                       'O':(-3.586, 'eV/molecule'),
+                       'N':(-4.352, 'eV/molecule'),
                        }
     if not isinstance(bindingEnergies, dict): raise InputError("bindingEnergies should be None (for default) or a dict.")
     newDict = {}
-    for element in 'CHO':
+    for element in 'CHON':
         try:
             newDict[element] = Energy(bindingEnergies[element])
         except KeyError: